{"id":"https://openalex.org/W2079807819","doi":"https://doi.org/10.1117/12.2042895","title":"3D reconstruction of digitized histological sections for vasculature quantification in the mouse hind limb","display_name":"3D reconstruction of digitized histological sections for vasculature quantification in the mouse hind limb","publication_year":2014,"publication_date":"2014-03-20","ids":{"openalex":"https://openalex.org/W2079807819","doi":"https://doi.org/10.1117/12.2042895","mag":"2079807819"},"language":"en","primary_location":{"id":"doi:10.1117/12.2042895","is_oa":false,"landing_page_url":"https://doi.org/10.1117/12.2042895","pdf_url":null,"source":{"id":"https://openalex.org/S183492911","display_name":"Proceedings of SPIE, the International Society for Optical Engineering/Proceedings of SPIE","issn_l":"0277-786X","issn":["0277-786X","1996-756X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310315543","host_organization_name":"SPIE","host_organization_lineage":["https://openalex.org/P4310315543"],"host_organization_lineage_names":["SPIE"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"SPIE Proceedings","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5083904441","display_name":"Yiwen Xu","orcid":"https://orcid.org/0000-0003-0509-7350"},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Yiwen Xu","raw_affiliation_strings":["The Univ. of Western Ontario (Canada)","The University of Western Ontario, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Univ. of Western Ontario (Canada)","institution_ids":["https://openalex.org/I125749732"]},{"raw_affiliation_string":"The University of Western Ontario, Canada","institution_ids":["https://openalex.org/I125749732"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026289208","display_name":"J. Geoffrey Pickering","orcid":"https://orcid.org/0000-0001-6474-3274"},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]},{"id":"https://openalex.org/I4210105758","display_name":"Robarts Clinical Trials","ror":"https://ror.org/01e36dv41","country_code":"CA","type":"facility","lineage":["https://openalex.org/I125749732","https://openalex.org/I4210105758","https://openalex.org/I4405252475"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"J. Geoffrey Pickering","raw_affiliation_strings":["Robarts Research Institute (Canada)","The Univ. of Western Ontario (Canada)","Robarts Research Institute  (Canada)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Robarts Research Institute (Canada)","institution_ids":["https://openalex.org/I4210105758"]},{"raw_affiliation_string":"The Univ. of Western Ontario (Canada)","institution_ids":["https://openalex.org/I125749732"]},{"raw_affiliation_string":"Robarts Research Institute  (Canada)","institution_ids":["https://openalex.org/I4210105758"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100910585","display_name":"Zengxuan Nong","orcid":null},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Zengxuan Nong","raw_affiliation_strings":["The Univ. of Western Ontario (Canada)","The University of Western Ontario, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Univ. of Western Ontario (Canada)","institution_ids":["https://openalex.org/I125749732"]},{"raw_affiliation_string":"The University of Western Ontario, Canada","institution_ids":["https://openalex.org/I125749732"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025274219","display_name":"Eli Gibson","orcid":"https://orcid.org/0000-0001-9207-7280"},"institutions":[{"id":"https://openalex.org/I4210105758","display_name":"Robarts Clinical Trials","ror":"https://ror.org/01e36dv41","country_code":"CA","type":"facility","lineage":["https://openalex.org/I125749732","https://openalex.org/I4210105758","https://openalex.org/I4405252475"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Eli Gibson","raw_affiliation_strings":["Robarts Research Institute (Canada)","#N##TAB##TAB##TAB##TAB# Robarts Research Institute, Canada#N##TAB##TAB##TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Robarts Research Institute (Canada)","institution_ids":["https://openalex.org/I4210105758"]},{"raw_affiliation_string":"#N##TAB##TAB##TAB##TAB# Robarts Research Institute, Canada#N##TAB##TAB##TAB#","institution_ids":["https://openalex.org/I4210105758"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5113914224","display_name":"Aaron D. Ward","orcid":null},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Aaron D. Ward","raw_affiliation_strings":["The Univ. of Western Ontario (Canada)","The University of Western Ontario, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Univ. of Western Ontario (Canada)","institution_ids":["https://openalex.org/I125749732"]},{"raw_affiliation_string":"The University of Western Ontario, Canada","institution_ids":["https://openalex.org/I125749732"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.1879,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.56728714,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"9041","issue":null,"first_page":"90410G","last_page":"90410G"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11984","display_name":"Anatomy and Medical Technology","score":0.9962999820709229,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11984","display_name":"Anatomy and Medical Technology","score":0.9962999820709229,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T14510","display_name":"Medical Imaging and Analysis","score":0.9861000180244446,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11227","display_name":"Diabetic Foot Ulcer Assessment and Management","score":0.9402999877929688,"subfield":{"id":"https://openalex.org/subfields/2712","display_name":"Endocrinology, Diabetes and Metabolism"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/hindlimb","display_name":"Hindlimb","score":0.7451941967010498},{"id":"https://openalex.org/keywords/anatomy","display_name":"Anatomy","score":0.49219003319740295},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4135599434375763},{"id":"https://openalex.org/keywords/biomedical-engineering","display_name":"Biomedical engineering","score":0.3235030472278595},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24770337343215942},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.24311843514442444}],"concepts":[{"id":"https://openalex.org/C51738704","wikidata":"https://www.wikidata.org/wiki/Q5766112","display_name":"Hindlimb","level":2,"score":0.7451941967010498},{"id":"https://openalex.org/C105702510","wikidata":"https://www.wikidata.org/wiki/Q514","display_name":"Anatomy","level":1,"score":0.49219003319740295},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4135599434375763},{"id":"https://openalex.org/C136229726","wikidata":"https://www.wikidata.org/wiki/Q327092","display_name":"Biomedical engineering","level":1,"score":0.3235030472278595},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24770337343215942},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.24311843514442444}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1117/12.2042895","is_oa":false,"landing_page_url":"https://doi.org/10.1117/12.2042895","pdf_url":null,"source":{"id":"https://openalex.org/S183492911","display_name":"Proceedings of SPIE, the International Society for Optical Engineering/Proceedings of SPIE","issn_l":"0277-786X","issn":["0277-786X","1996-756X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310315543","host_organization_name":"SPIE","host_organization_lineage":["https://openalex.org/P4310315543"],"host_organization_lineage_names":["SPIE"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"SPIE Proceedings","raw_type":"proceedings-article"},{"id":"pmh:oai:eprints.ucl.ac.uk.OAI2:1518258","is_oa":false,"landing_page_url":"http://discovery.ucl.ac.uk/1518258/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400024","display_name":"UCL Discovery (University College London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I45129253","host_organization_name":"University College London","host_organization_lineage":["https://openalex.org/I45129253"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"     In: Gurcan, MN and Madabhushi, A, (eds.)  (Proceedings) 2nd Conference on Medical Imaging - Digital Pathology.   SPIE-INT SOC OPTICAL ENGINEERING (2014)     ","raw_type":"Proceedings paper"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":15,"referenced_works":["https://openalex.org/W1966030161","https://openalex.org/W1996883058","https://openalex.org/W2026616100","https://openalex.org/W2036239622","https://openalex.org/W2049981393","https://openalex.org/W2056414826","https://openalex.org/W2074079901","https://openalex.org/W2086374737","https://openalex.org/W2088526319","https://openalex.org/W2121075186","https://openalex.org/W2129916129","https://openalex.org/W2133059825","https://openalex.org/W2139479159","https://openalex.org/W2158008371","https://openalex.org/W6668906776"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2087719526","https://openalex.org/W2063133063","https://openalex.org/W2113590032","https://openalex.org/W2390279801","https://openalex.org/W1748928841","https://openalex.org/W1878020629","https://openalex.org/W2358668433","https://openalex.org/W2426807744"],"abstract_inverted_index":{"In":[0],"contrast":[1],"to":[2,53,71,142,150,180,200,209],"imaging":[3,9,251],"modalities":[4],"such":[5],"as":[6],"magnetic":[7],"resonance":[8],"and":[10,36,45,60,97,178,212,228,235,241,258],"micro":[11],"computed":[12],"tomography,":[13],"digital":[14],"histology":[15,31,79,250],"reveals":[16],"multiple":[17],"stained":[18,94],"tissue":[19,41,80],"features":[20],"at":[21,120],"high":[22],"resolution":[23],"(0.25μm/pixel).":[24],"However,":[25],"the":[26,39,54,82,87,92,127,182,224,229],"two-dimensional":[27],"(2D)":[28],"nature":[29],"of":[30,38,67,78,91,113,147,167,246],"challenges":[32],"three-dimensional":[33],"(3D)":[34],"quantification":[35],"visualization":[37],"different":[40],"components,":[42],"cellular":[43],"structures,":[44],"subcellular":[46],"elements.":[47],"This":[48],"limitation":[49],"is":[50,252],"particularly":[51],"relevant":[52],"vasculature,":[55],"which":[56,203],"has":[57],"a":[58,73,106,143,151,168],"complex":[59],"variable":[61],"structure":[62],"within":[63],"tissues.":[64],"The":[65,214],"objective":[66],"this":[68,158],"study":[69],"was":[70,124,161],"perform":[72],"fully":[74],"automated":[75],"3D":[76,107,243],"reconstruction":[77,108,245],"in":[81,154],"mouse":[83,247],"hind":[84,248],"limb":[85,249],"preserving":[86],"accurate":[88,242],"systemic":[89],"orientation":[90],"tissues,":[93],"with":[95],"hematoxylin":[96],"immunostained":[98],"for":[99,223],"smooth":[100],"muscle":[101],"\u03b1":[102],"actin.":[103],"We":[104],"performed":[105,125],"using":[109,126],"pairwise":[110],"rigid":[111,244],"registrations":[112,202],"5μm":[114],"thick,":[115],"paraffin-embedded":[116],"serial":[117],"sections,":[118],"digitized":[119],"0.25μm/pixel.":[121],"Each":[122],"registration":[123,218],"iterative":[128],"closest":[129],"points":[130],"algorithm":[131],"on":[132,164,191,255],"blood":[133],"vessel":[134,138,183,225],"landmarks.":[135],"Landmarks":[136],"were":[137,174,198,233],"centroids,":[139],"determined":[140,162],"according":[141],"signed":[144],"distance":[145],"map":[146],"each":[148],"pixel":[149],"decision":[152,159],"boundary":[153,160],"hue-saturation-value":[155],"color":[156],"space;":[157],"based":[163,254],"manual":[165],"annotation":[166],"separate":[169],"training":[170],"set.":[171],"Cell":[172],"nuclei":[173],"then":[175],"automatically":[176],"extracted":[177,256],"corresponded":[179],"refine":[181],"landmark":[184,188,226,231],"registration.":[185],"Homologous":[186],"nucleus":[187,230],"pairs":[189],"appearing":[190],"not":[192],"more":[193],"than":[194],"two":[195],"adjacent":[196],"slides":[197],"chosen":[199],"avoid":[201],"force":[204],"curved":[205],"or":[206],"non-sectionorthogonal":[207],"structures":[208],"be":[210],"straight":[211],"section-orthogonal.":[213],"median":[215],"accumulated":[216],"target":[217],"errors":[219],"\u00b1":[220],"interquartile":[221],"ranges":[222],"registration,":[227],"refinement":[232],"43.4±42.8μm":[234],"2.9±1.7μm,":[236],"respectively":[237],"(p<0.0001).":[238],"Fully":[239],"automatic":[240],"feasible":[253],"vasculature":[257],"nuclei.":[259]},"counts_by_year":[{"year":2015,"cited_by_count":1}],"updated_date":"2026-07-02T09:51:11.867554","created_date":"2025-10-10T00:00:00"}